What is the issue?
When wie calculate the absolute position of a crosslink for its validation, we are off by one. If we use the position to calculate the exact amino acid from the whole protein sequence, this amino acid does not match the one that was originally desired in the data (for the XLinkX data format we actually see the peptide sequence with the exact amino acid marked). (Note that both the position within the peptide and the absolute position within the protein are 1-based)
How to reproduce the issue?
Do a validation and get the crosslinker table. Then get the protein sequence from the fasta and get the amino acid at the crosslinker position (one letter). Then find the peptide sequence of the binding site of this crosslinker in the crosslinking data and see which letter is marked there.
What is the expected behavior?
The amino acid at the position of the crosslinker we calculated should match the amino acid desired in the data.
What is the issue?
When wie calculate the absolute position of a crosslink for its validation, we are off by one. If we use the position to calculate the exact amino acid from the whole protein sequence, this amino acid does not match the one that was originally desired in the data (for the XLinkX data format we actually see the peptide sequence with the exact amino acid marked). (Note that both the position within the peptide and the absolute position within the protein are 1-based)
How to reproduce the issue?
Do a validation and get the crosslinker table. Then get the protein sequence from the fasta and get the amino acid at the crosslinker position (one letter). Then find the peptide sequence of the binding site of this crosslinker in the crosslinking data and see which letter is marked there.
What is the expected behavior?
The amino acid at the position of the crosslinker we calculated should match the amino acid desired in the data.